HEADER TRANSCRIPTION 11-DEC-19 6TOK TITLE CRYSTAL STRUCTURE OF HUMAN BCL6 BTB DOMAIN IN COMPLEX WITH COMPOUND TITLE 2 23D COMPND MOL_ID: 1; COMPND 2 MOLECULE: B-CELL LYMPHOMA 6 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BCL-6,B-CELL LYMPHOMA 5 PROTEIN,BCL-5,PROTEIN LAZ-3,ZINC COMPND 5 FINGER AND BTB DOMAIN-CONTAINING PROTEIN 27,ZINC FINGER PROTEIN 51; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ALA-TRP-VAL-ILE-PRO-ALA; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BCL6, BCL5, LAZ3, ZBTB27, ZNF51; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: AI; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET48B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS CANCER, LYMPHOMA, INHIBITOR, DEGRADER, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR M.J.RODRIGUES,Y.-V.LE BIHAN,R.L.M.VAN MONTFORT REVDAT 3 24-JAN-24 6TOK 1 REMARK REVDAT 2 06-MAY-20 6TOK 1 JRNL REVDAT 1 22-APR-20 6TOK 0 JRNL AUTH B.R.BELLENIE,K.J.CHEUNG,A.VARELA,O.A.PIERRAT,G.W.COLLIE, JRNL AUTH 2 G.M.BOX,M.D.BRIGHT,S.GOWAN,A.HAYES,M.J.RODRIGUES,K.N.SHETTY, JRNL AUTH 3 M.CARTER,O.A.DAVIS,A.T.HENLEY,P.INNOCENTI,L.D.JOHNSON,M.LIU, JRNL AUTH 4 S.DE KLERK,Y.V.LE BIHAN,M.G.LLOYD,P.C.MCANDREW,E.SHEHU, JRNL AUTH 5 R.TALBOT,H.L.WOODWARD,R.BURKE,V.KIRKIN,R.L.M.VAN MONTFORT, JRNL AUTH 6 F.I.RAYNAUD,O.W.ROSSANESE,S.HOELDER JRNL TITL ACHIEVINGIN VIVOTARGET DEPLETION THROUGH THE DISCOVERY AND JRNL TITL 2 OPTIMIZATION OF BENZIMIDAZOLONE BCL6 DEGRADERS. JRNL REF J.MED.CHEM. V. 63 4047 2020 JRNL REFN ISSN 0022-2623 JRNL PMID 32275432 JRNL DOI 10.1021/ACS.JMEDCHEM.9B02076 REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 44230 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 2204 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 50 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.43 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 885 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2466 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 847 REMARK 3 BIN R VALUE (WORKING SET) : 0.2463 REMARK 3 BIN FREE R VALUE : 0.2545 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.29 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 38 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1021 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 178 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.26890 REMARK 3 B22 (A**2) : -1.26890 REMARK 3 B33 (A**2) : 2.53780 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.180 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.055 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.052 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.050 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.048 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1274 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1716 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 449 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 243 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1274 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 161 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : 18 ; 1.000 ; HARMONIC REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1500 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 0.97 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.30 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 13.34 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|5 - 33} REMARK 3 ORIGIN FOR THE GROUP (A): 31.3795 -27.0999 13.3216 REMARK 3 T TENSOR REMARK 3 T11: -0.0360 T22: -0.0264 REMARK 3 T33: -0.0317 T12: -0.0151 REMARK 3 T13: -0.0012 T23: -0.0266 REMARK 3 L TENSOR REMARK 3 L11: 2.4675 L22: 1.4993 REMARK 3 L33: 3.3634 L12: 0.3636 REMARK 3 L13: 0.3312 L23: 0.8936 REMARK 3 S TENSOR REMARK 3 S11: 0.1201 S12: 0.1416 S13: -0.1945 REMARK 3 S21: 0.1911 S22: 0.0021 S23: -0.0800 REMARK 3 S31: 0.3231 S32: -0.1173 S33: -0.1222 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|34 - 46} REMARK 3 ORIGIN FOR THE GROUP (A): 39.9859 -13.7326 31.8488 REMARK 3 T TENSOR REMARK 3 T11: 0.0256 T22: -0.0381 REMARK 3 T33: -0.0951 T12: -0.0641 REMARK 3 T13: -0.0180 T23: -0.0643 REMARK 3 L TENSOR REMARK 3 L11: 1.8505 L22: 1.6004 REMARK 3 L33: 0.9289 L12: -0.2390 REMARK 3 L13: 0.9053 L23: 0.0484 REMARK 3 S TENSOR REMARK 3 S11: 0.0844 S12: -0.3649 S13: 0.1412 REMARK 3 S21: 0.5099 S22: 0.1056 S23: -0.1466 REMARK 3 S31: -0.1339 S32: 0.2692 S33: -0.1900 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {A|47 - 92} REMARK 3 ORIGIN FOR THE GROUP (A): 33.5613 -11.0081 24.5339 REMARK 3 T TENSOR REMARK 3 T11: 0.0187 T22: -0.0705 REMARK 3 T33: -0.0193 T12: -0.0496 REMARK 3 T13: 0.0413 T23: -0.0281 REMARK 3 L TENSOR REMARK 3 L11: 1.2940 L22: 2.7006 REMARK 3 L33: 2.5439 L12: 0.9262 REMARK 3 L13: -0.2574 L23: 1.1439 REMARK 3 S TENSOR REMARK 3 S11: 0.2020 S12: -0.0641 S13: 0.1313 REMARK 3 S21: 0.1813 S22: -0.0304 S23: -0.0466 REMARK 3 S31: -0.2948 S32: 0.0505 S33: -0.1716 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: {A|93 - 101} REMARK 3 ORIGIN FOR THE GROUP (A): 22.6734 -23.8870 32.3572 REMARK 3 T TENSOR REMARK 3 T11: 0.1252 T22: 0.0150 REMARK 3 T33: -0.0437 T12: -0.1404 REMARK 3 T13: 0.0621 T23: -0.0277 REMARK 3 L TENSOR REMARK 3 L11: 3.5681 L22: 1.2931 REMARK 3 L33: 1.1146 L12: 1.5832 REMARK 3 L13: -0.7176 L23: -2.8038 REMARK 3 S TENSOR REMARK 3 S11: 0.2048 S12: -0.3213 S13: -0.0456 REMARK 3 S21: 0.3332 S22: -0.2843 S23: 0.2019 REMARK 3 S31: 0.0939 S32: 0.1285 S33: 0.0795 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: {A|102 - 114} REMARK 3 ORIGIN FOR THE GROUP (A): 23.5941 -10.8914 31.4441 REMARK 3 T TENSOR REMARK 3 T11: 0.0131 T22: -0.0687 REMARK 3 T33: -0.0353 T12: -0.0601 REMARK 3 T13: 0.1112 T23: -0.0690 REMARK 3 L TENSOR REMARK 3 L11: 1.2959 L22: 3.8541 REMARK 3 L33: 3.7187 L12: 1.3738 REMARK 3 L13: 0.9101 L23: 1.1848 REMARK 3 S TENSOR REMARK 3 S11: 0.2656 S12: -0.2204 S13: 0.2663 REMARK 3 S21: 0.5148 S22: -0.3075 S23: 0.4874 REMARK 3 S31: -0.1089 S32: -0.5791 S33: 0.0419 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: {A|115 - 129} REMARK 3 ORIGIN FOR THE GROUP (A): 13.5219 -15.0141 31.8140 REMARK 3 T TENSOR REMARK 3 T11: -0.0059 T22: 0.0865 REMARK 3 T33: 0.0576 T12: -0.0771 REMARK 3 T13: 0.1345 T23: -0.0978 REMARK 3 L TENSOR REMARK 3 L11: 5.0051 L22: 2.9793 REMARK 3 L33: 0.0000 L12: -1.2303 REMARK 3 L13: -3.5724 L23: 0.9638 REMARK 3 S TENSOR REMARK 3 S11: 0.0021 S12: 0.0922 S13: 0.0251 REMARK 3 S21: 0.2848 S22: -0.1780 S23: 0.4094 REMARK 3 S31: 0.0956 S32: -0.3069 S33: 0.1759 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: {B|0 - 5} REMARK 3 ORIGIN FOR THE GROUP (A): 19.1649 -32.9476 2.1158 REMARK 3 T TENSOR REMARK 3 T11: -0.0973 T22: 0.1261 REMARK 3 T33: -0.0280 T12: -0.0618 REMARK 3 T13: -0.0289 T23: -0.0873 REMARK 3 L TENSOR REMARK 3 L11: 1.9057 L22: 0.5761 REMARK 3 L33: 0.5224 L12: 0.8455 REMARK 3 L13: -0.6069 L23: 0.4959 REMARK 3 S TENSOR REMARK 3 S11: 0.0514 S12: 0.0323 S13: 0.0367 REMARK 3 S21: -0.0292 S22: -0.0033 S23: 0.0125 REMARK 3 S31: 0.1322 S32: 0.0141 S33: -0.0481 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6TOK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1292104969. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9282 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44308 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 59.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.70 REMARK 200 R MERGE FOR SHELL (I) : 3.26200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3BIM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 MICROLITER OF THE BCL6-BTB/WVIP REMARK 280 COMPLEX AT 4 MG/ML PLUS 1 MICROLITER OF A CRYSTALLISATION REMARK 280 SOLUTION CONSISTING OF 1 M K2HPO4, 0.7 M NAH2PO4, 75 MM SODIUM REMARK 280 ACETATE BUFFER PH 4.5 AND 2 % DMSO, AGAINST 350 MICROLITER OF REMARK 280 CRYSTALLISATION SOLUTION., PH 7, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.24233 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 112.48467 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 84.36350 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 140.60583 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.12117 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 56.24233 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 112.48467 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 140.60583 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 84.36350 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 28.12117 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.500000 0.866025 0.000000 34.29700 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -59.40415 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 28.12117 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 445 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 463 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 2 REMARK 465 PRO A 3 REMARK 465 GLY A 4 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 13 NE CZ NH1 NH2 REMARK 470 GLN A 64 CD OE1 NE2 REMARK 470 GLU A 77 CD OE1 OE2 REMARK 470 GLU A 99 OE2 REMARK 470 LYS A 123 NZ REMARK 470 LYS A 126 CD CE NZ REMARK 470 GLU A 129 O REMARK 470 ALA B 0 N CB REMARK 470 ALA B 5 CA C O CB REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 39 -127.87 61.66 REMARK 500 SER A 93 -3.07 79.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NQT A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 101 DBREF 6TOK A 5 129 UNP P41182 BCL6_HUMAN 5 129 DBREF 6TOK B 0 5 PDB 6TOK 6TOK 0 5 SEQADV 6TOK GLY A 2 UNP P41182 EXPRESSION TAG SEQADV 6TOK PRO A 3 UNP P41182 EXPRESSION TAG SEQADV 6TOK GLY A 4 UNP P41182 EXPRESSION TAG SEQRES 1 A 128 GLY PRO GLY ALA ASP SER CYS ILE GLN PHE THR ARG HIS SEQRES 2 A 128 ALA SER ASP VAL LEU LEU ASN LEU ASN ARG LEU ARG SER SEQRES 3 A 128 ARG ASP ILE LEU THR ASP VAL VAL ILE VAL VAL SER ARG SEQRES 4 A 128 GLU GLN PHE ARG ALA HIS LYS THR VAL LEU MET ALA CYS SEQRES 5 A 128 SER GLY LEU PHE TYR SER ILE PHE THR ASP GLN LEU LYS SEQRES 6 A 128 CYS ASN LEU SER VAL ILE ASN LEU ASP PRO GLU ILE ASN SEQRES 7 A 128 PRO GLU GLY PHE CYS ILE LEU LEU ASP PHE MET TYR THR SEQRES 8 A 128 SER ARG LEU ASN LEU ARG GLU GLY ASN ILE MET ALA VAL SEQRES 9 A 128 MET ALA THR ALA MET TYR LEU GLN MET GLU HIS VAL VAL SEQRES 10 A 128 ASP THR CYS ARG LYS PHE ILE LYS ALA SER GLU SEQRES 1 B 6 ALA TRP VAL ILE PRO ALA HET NQT A 201 32 HET EDO A 202 4 HET EDO A 203 4 HET EDO A 204 8 HET EDO A 205 4 HET EDO A 206 4 HET EDO A 207 4 HET EDO A 208 4 HET EDO A 209 4 HET EDO A 210 4 HET EDO A 211 4 HET EDO A 212 4 HET EDO A 213 4 HET DMS A 214 4 HET DMS A 215 4 HET DMS A 216 4 HET DMS B 101 4 HETNAM NQT 5-[[5-CHLORANYL-2-(3,5-DIMETHYLPYRAZOL-1-YL)PYRIMIDIN- HETNAM 2 NQT 4-YL]AMINO]-1-METHYL-3-(3-METHYL-3-OXIDANYL-BUTYL) HETNAM 3 NQT BENZIMIDAZOL-2-ONE HETNAM EDO 1,2-ETHANEDIOL HETNAM DMS DIMETHYL SULFOXIDE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 NQT C22 H26 CL N7 O2 FORMUL 4 EDO 12(C2 H6 O2) FORMUL 16 DMS 4(C2 H6 O S) FORMUL 20 HOH *178(H2 O) HELIX 1 AA1 ARG A 13 ARG A 28 1 16 HELIX 2 AA2 HIS A 46 SER A 54 1 9 HELIX 3 AA3 SER A 54 THR A 62 1 9 HELIX 4 AA4 LEU A 65 LEU A 69 5 5 HELIX 5 AA5 ASN A 79 SER A 93 1 15 HELIX 6 AA6 ASN A 101 GLN A 113 1 13 HELIX 7 AA7 MET A 114 GLU A 129 1 16 SHEET 1 AA1 2 GLN A 10 PHE A 11 0 SHEET 2 AA1 2 TRP B 1 VAL B 2 -1 O VAL B 2 N GLN A 10 SHEET 1 AA2 3 GLU A 41 ALA A 45 0 SHEET 2 AA2 3 VAL A 34 VAL A 38 -1 N ILE A 36 O PHE A 43 SHEET 3 AA2 3 VAL A 71 ASN A 73 1 O ILE A 72 N VAL A 37 SITE 1 AC1 17 ASP A 17 ASN A 21 ARG A 24 LEU A 25 SITE 2 AC1 17 ARG A 28 MET A 51 ALA A 52 CYS A 53 SITE 3 AC1 17 GLY A 55 TYR A 58 GLN A 113 GLU A 115 SITE 4 AC1 17 EDO A 206 EDO A 213 HOH A 348 HOH A 350 SITE 5 AC1 17 HOH A 381 SITE 1 AC2 4 ASP A 63 GLN A 64 ARG A 98 GLU A 99 SITE 1 AC3 4 ARG A 28 ASP A 29 HOH A 331 HOH A 369 SITE 1 AC4 6 ASP A 75 ILE A 78 TYR A 111 EDO A 208 SITE 2 AC4 6 HOH A 385 ALA B 5 SITE 1 AC5 2 ILE A 125 SER A 128 SITE 1 AC6 4 GLU A 115 HIS A 116 NQT A 201 HOH A 318 SITE 1 AC7 4 SER A 16 ASP A 17 HOH A 330 HOH A 371 SITE 1 AC8 2 ARG A 94 EDO A 204 SITE 1 AC9 4 GLU A 41 GLN A 42 PHE A 43 DMS A 214 SITE 1 AD1 3 ARG A 26 ASP A 29 ARG A 44 SITE 1 AD2 3 ARG A 24 EDO A 212 DMS A 215 SITE 1 AD3 5 SER A 27 ARG A 28 EDO A 211 DMS A 215 SITE 2 AD3 5 HOH A 301 SITE 1 AD4 3 TYR A 58 NQT A 201 HOH A 337 SITE 1 AD5 2 GLU A 41 EDO A 209 SITE 1 AD6 4 ASN A 23 SER A 27 EDO A 211 EDO A 212 SITE 1 AD7 5 LEU A 69 SER A 70 VAL A 71 HOH A 342 SITE 2 AD7 5 HOH A 425 SITE 1 AD8 4 VAL A 71 ILE A 72 ASN A 73 TRP B 1 CRYST1 68.594 68.594 168.727 90.00 90.00 120.00 P 61 2 2 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014579 0.008417 0.000000 0.00000 SCALE2 0.000000 0.016834 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005927 0.00000